/*
 * Copyright (c) 2016. Real Time Genomics Limited.
 *
 * All rights reserved.
 *
 * Redistribution and use in source and binary forms, with or without
 * modification, are permitted provided that the following conditions are
 * met:
 *
 * 1. Redistributions of source code must retain the above copyright
 *    notice, this list of conditions and the following disclaimer.
 *
 * 2. Redistributions in binary form must reproduce the above copyright
 *    notice, this list of conditions and the following disclaimer in the
 *    documentation and/or other materials provided with the
 *    distribution.
 *
 * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
 * "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
 * LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
 * A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
 * HOLDER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
 * SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
 * LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
 * DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
 * THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
 * (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
 * OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
 */
package com.rtg.vcf;

import com.rtg.vcf.header.VcfHeader;

/**
 * Not a filter as such, but produces an end-user exception if out-of-order records are encountered.
 * Does not check that chromosomes appear in any particular order, only checks record positions within
 * the same chromosome.
 */
public class AssertVcfSorted implements VcfFilter {

  private String mLastSeq = null;
  private int mLastStart = 0;

  @Override
  public void setHeader(VcfHeader header) { }

  @Override
  public boolean accept(VcfRecord rec) {
    if (rec.getSequenceName().equals(mLastSeq) && rec.getStart() < mLastStart) {
      throw new VcfFormatException("VCF is not sorted (previous start = " + (mLastStart + 1) + "), at record: " + rec);
    }
    mLastSeq = rec.getSequenceName();
    mLastStart = rec.getStart();
    return true;
  }
}
